Job ID = 9029487 sra ファイルのダウンロード中... Completed: 258888K bytes transferred in 5 seconds (416867K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 7663 0 7663 0 0 1085 0 --:--:-- 0:00:07 --:--:-- 11610 100 38318 0 38318 0 0 4757 0 --:--:-- 0:00:08 --:--:-- 23152 100 51919 0 51919 0 0 6286 0 --:--:-- 0:00:08 --:--:-- 27898 sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 10194272 spots for /home/okishinya/chipatlas/results/dm3/SRX1794240/SRR3575283.sra Written 10194272 spots total rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:39 10194272 reads; of these: 10194272 (100.00%) were unpaired; of these: 276781 (2.72%) aligned 0 times 7222828 (70.85%) aligned exactly 1 time 2694663 (26.43%) aligned >1 times 97.28% overall alignment rate Time searching: 00:03:39 Overall time: 00:03:39 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 464852 / 9917491 = 0.0469 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sat, 03 Jun 2017 14:00:48: # Command line: callpeak -t SRX1794240.bam -f BAM -g dm -n SRX1794240.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1794240.10 # format = BAM # ChIP-seq file = ['SRX1794240.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Sat, 03 Jun 2017 14:00:48: # Command line: callpeak -t SRX1794240.bam -f BAM -g dm -n SRX1794240.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1794240.20 # format = BAM # ChIP-seq file = ['SRX1794240.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Sat, 03 Jun 2017 14:00:48: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:00:48: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:00:48: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:00:48: # Command line: callpeak -t SRX1794240.bam -f BAM -g dm -n SRX1794240.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1794240.05 # format = BAM # ChIP-seq file = ['SRX1794240.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Sat, 03 Jun 2017 14:00:48: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:00:48: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:00:48: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:00:53: 1000000 INFO @ Sat, 03 Jun 2017 14:00:53: 1000000 INFO @ Sat, 03 Jun 2017 14:00:54: 1000000 INFO @ Sat, 03 Jun 2017 14:00:59: 2000000 INFO @ Sat, 03 Jun 2017 14:00:59: 2000000 INFO @ Sat, 03 Jun 2017 14:00:59: 2000000 INFO @ Sat, 03 Jun 2017 14:01:04: 3000000 INFO @ Sat, 03 Jun 2017 14:01:05: 3000000 INFO @ Sat, 03 Jun 2017 14:01:05: 3000000 INFO @ Sat, 03 Jun 2017 14:01:10: 4000000 INFO @ Sat, 03 Jun 2017 14:01:11: 4000000 INFO @ Sat, 03 Jun 2017 14:01:11: 4000000 INFO @ Sat, 03 Jun 2017 14:01:16: 5000000 INFO @ Sat, 03 Jun 2017 14:01:17: 5000000 INFO @ Sat, 03 Jun 2017 14:01:17: 5000000 INFO @ Sat, 03 Jun 2017 14:01:22: 6000000 INFO @ Sat, 03 Jun 2017 14:01:23: 6000000 INFO @ Sat, 03 Jun 2017 14:01:23: 6000000 INFO @ Sat, 03 Jun 2017 14:01:28: 7000000 INFO @ Sat, 03 Jun 2017 14:01:29: 7000000 INFO @ Sat, 03 Jun 2017 14:01:29: 7000000 INFO @ Sat, 03 Jun 2017 14:01:34: 8000000 INFO @ Sat, 03 Jun 2017 14:01:35: 8000000 INFO @ Sat, 03 Jun 2017 14:01:35: 8000000 INFO @ Sat, 03 Jun 2017 14:01:39: 9000000 INFO @ Sat, 03 Jun 2017 14:01:40: 9000000 INFO @ Sat, 03 Jun 2017 14:01:41: 9000000 INFO @ Sat, 03 Jun 2017 14:01:42: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:01:42: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:01:42: #1 total tags in treatment: 9452639 INFO @ Sat, 03 Jun 2017 14:01:42: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:01:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:01:43: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:01:43: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:01:43: #1 total tags in treatment: 9452639 INFO @ Sat, 03 Jun 2017 14:01:43: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:01:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:01:44: #1 tags after filtering in treatment: 9451637 INFO @ Sat, 03 Jun 2017 14:01:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:01:44: #1 finished! INFO @ Sat, 03 Jun 2017 14:01:44: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:01:44: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:01:44: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:01:44: #1 total tags in treatment: 9452639 INFO @ Sat, 03 Jun 2017 14:01:44: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:01:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:01:45: #1 tags after filtering in treatment: 9451637 INFO @ Sat, 03 Jun 2017 14:01:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:01:45: #1 finished! INFO @ Sat, 03 Jun 2017 14:01:45: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:01:46: #2 number of paired peaks: 504 WARNING @ Sat, 03 Jun 2017 14:01:46: Fewer paired peaks (504) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 504 pairs to build model! INFO @ Sat, 03 Jun 2017 14:01:46: start model_add_line... INFO @ Sat, 03 Jun 2017 14:01:46: #1 tags after filtering in treatment: 9451637 INFO @ Sat, 03 Jun 2017 14:01:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:01:46: #1 finished! INFO @ Sat, 03 Jun 2017 14:01:46: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:01:47: #2 number of paired peaks: 504 WARNING @ Sat, 03 Jun 2017 14:01:47: Fewer paired peaks (504) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 504 pairs to build model! INFO @ Sat, 03 Jun 2017 14:01:47: start model_add_line... INFO @ Sat, 03 Jun 2017 14:01:48: #2 number of paired peaks: 504 WARNING @ Sat, 03 Jun 2017 14:01:48: Fewer paired peaks (504) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 504 pairs to build model! INFO @ Sat, 03 Jun 2017 14:01:48: start model_add_line... INFO @ Sat, 03 Jun 2017 14:01:49: start X-correlation... INFO @ Sat, 03 Jun 2017 14:01:50: end of X-cor INFO @ Sat, 03 Jun 2017 14:01:50: #2 finished! INFO @ Sat, 03 Jun 2017 14:01:50: #2 predicted fragment length is 53 bps INFO @ Sat, 03 Jun 2017 14:01:50: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sat, 03 Jun 2017 14:01:50: #2.2 Generate R script for model : SRX1794240.10_model.r WARNING @ Sat, 03 Jun 2017 14:01:50: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:01:50: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sat, 03 Jun 2017 14:01:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 14:01:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:01:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:01:50: start X-correlation... INFO @ Sat, 03 Jun 2017 14:01:50: end of X-cor INFO @ Sat, 03 Jun 2017 14:01:50: #2 finished! INFO @ Sat, 03 Jun 2017 14:01:50: #2 predicted fragment length is 53 bps INFO @ Sat, 03 Jun 2017 14:01:50: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sat, 03 Jun 2017 14:01:50: #2.2 Generate R script for model : SRX1794240.20_model.r WARNING @ Sat, 03 Jun 2017 14:01:50: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:01:50: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sat, 03 Jun 2017 14:01:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 14:01:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:01:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:01:52: start X-correlation... INFO @ Sat, 03 Jun 2017 14:01:52: end of X-cor INFO @ Sat, 03 Jun 2017 14:01:52: #2 finished! INFO @ Sat, 03 Jun 2017 14:01:52: #2 predicted fragment length is 53 bps INFO @ Sat, 03 Jun 2017 14:01:52: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sat, 03 Jun 2017 14:01:52: #2.2 Generate R script for model : SRX1794240.05_model.r WARNING @ Sat, 03 Jun 2017 14:01:52: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:01:52: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sat, 03 Jun 2017 14:01:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 14:01:52: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:01:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:02:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:02:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:02:49: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:03:22: #4 Write output xls file... SRX1794240.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:03:22: #4 Write peak in narrowPeak format file... SRX1794240.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:03:22: #4 Write summits bed file... SRX1794240.10_summits.bed INFO @ Sat, 03 Jun 2017 14:03:22: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (756 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:03:26: #4 Write output xls file... SRX1794240.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:03:26: #4 Write peak in narrowPeak format file... SRX1794240.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:03:26: #4 Write summits bed file... SRX1794240.05_summits.bed INFO @ Sat, 03 Jun 2017 14:03:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1864 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:03:30: #4 Write output xls file... SRX1794240.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:03:30: #4 Write peak in narrowPeak format file... SRX1794240.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:03:30: #4 Write summits bed file... SRX1794240.20_summits.bed INFO @ Sat, 03 Jun 2017 14:03:30: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (218 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。